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From: Juha H. <juh...@he...> - 2020-11-09 19:46:18
|
Hi Colin, Have you tried the 'extract coordinates' protocol? Best wishes, Juha On Mon, Nov 9, 2020 at 9:40 PM Colin Deniston <ckd...@gm...> wrote: > Hi, > > I'm processing some data and would like to re-extract a subset of > particles I've picked out after 2D classification. I can't find a way to do > this as Scipion seems to consider this subset as only particles, not > coordinates. Can you not re-extract in Scipion currently? Is the coordinate > info not held onto for each particle? Thanks. > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Colin D. <ckd...@gm...> - 2020-11-09 19:38:58
|
Hi, I'm processing some data and would like to re-extract a subset of particles I've picked out after 2D classification. I can't find a way to do this as Scipion seems to consider this subset as only particles, not coordinates. Can you not re-extract in Scipion currently? Is the coordinate info not held onto for each particle? Thanks. |
|
From: Grigory S. <sha...@gm...> - 2020-11-06 23:34:03
|
Hi, There's no such thing as a density threshold for 2D classification in relion, nor any projection operations. On Fri, Nov 6, 2020, 20:44 Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > I am kindly asking for your advice. > > > *What are the default parameters for visualizing the 2D class averages in > SCIPION and what is the default density threshold?* > > > > This question is connected to the possibility to see (or not) the > structures we are interested in on the 2D class averages, projected in > SCIPION. > > There is a doubt that if the density threshold differs for different 2D > class averages in the series of the 2D alignments, some parts of the > structure may not be visible and/or comparable. > > > > The 2D classifications were done using relion 2D classification protocol > inside the SCIPION. > > > Thank you in advance. > > > > Sincerely, > > Dmitry > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Dmitry A. S. <sem...@gm...> - 2020-11-06 20:44:36
|
Dear colleagues, I am kindly asking for your advice. What are the default parameters for visualizing the 2D class averages in SCIPION and what is the default density threshold? This question is connected to the possibility to see (or not) the structures we are interested in on the 2D class averages, projected in SCIPION. There is a doubt that if the density threshold differs for different 2D class averages in the series of the 2D alignments, some parts of the structure may not be visible and/or comparable. The 2D classifications were done using relion 2D classification protocol inside the SCIPION. Thank you in advance. Sincerely, Dmitry |
|
From: Pablo C. <pc...@cn...> - 2020-11-06 08:09:23
|
Hi Teige, I'm very happy to see your enthusiasm, thanks. As far as I know, unless there are some details I might be missing, you currently have (scipion3): gctf, relion, and cryosparc (in beta) Regarding Scipion not using gctf-1.06, default values point to 1.18. You may need: 1.- Install 1.0 binaries: *scipion3 installb gctf-1.06* 2.- Edit/create scipion-conf file: If you want to use a different binary then you need to have a scipion.conf file (optional and missing by default). Something like this placed on <SCIPION_HOME>/config/scipion.conf should be the minimal you need: -------------------scipion.conf file----------------- [PLUGINS] GCTF_HOME = /home/pablo/software/scipion/software/em/gctf-1.06 GCTF = Gctf-v1.06_sm_30_cu8.0_x86_64 GCTF_CUDA_LIB = /usr/local/cuda-8.0/lib64 --------------------------------------------------------- NOTE: Adapt the paths to your SCIPION_HOME and cuda version you want to use. To know which variables can be set for a specific plugin try: >> *scipion3 config -p gctf* Scipion v3.0.5 - Eugenius Variables defined by plugin 'gctf': GCTF_HOME = /home/pablo/software/scipion/software/em/gctf-1.18 GCTF = Gctf_v1.18_sm30-75_cu10.1 GCTF_CUDA_LIB = /usr/local/cuda/lib64 These variables can be added/edited in '/home/pablo/software/scipion/config/scipion.conf' Each plugin has it's small documentation page where these details are usually commented: See https://github.com/scipion-em/scipion-em-gctf Cheers, Pablo. On 6/11/20 7:54, Matthews-Palmer, Teige wrote: > Dear Scipion users & devs, > > I’m very excited to be installing Scipion v3.0.5 at a new job - it has been a while since I used Scipion and very many programs and features have been added, it looks wonderful. > > One feature I would really like to use in Scipion is accurate CTF estimation for particles on tilted micrographs. > As far as I know the options are patch-based CTF in gCTF (initially, before particle picking), per-particle in gCTF, geometry aware CTF in goCTF, and something similar in Warp. Maybe there are other options that I’m not aware of - I’d be happy to hear about them! > > It looks like local or per-particle CTF are not available with gCTF in Scipion3 - is that right? > > Using the plugin manager I installed gctf-1.18 > Then, since the github page mentions 1.18 is specifically for phase plate, I installed gctf-1.06 with the plugin manager - but the ProtGctf protocol in Scipion is not changed and still has no options relating to patch or per-particle CTF. > > So, can I get accurate particle defocus values from tilted data in a Scipion workflow? > > Many thanks, > Teige > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Grigory S. <sha...@gm...> - 2020-11-06 08:08:15
|
Hello, Teige, Gctf plugin uses Gctf 1.18 by default, so you need to create scipion config file and change Gctf variables there to point to the 1.06 version. Then you should see a second Gctf protocol in scipion. Grigory. On Fri, Nov 6, 2020, 06:55 Matthews-Palmer, Teige < t.m...@im...> wrote: > Dear Scipion users & devs, > > I’m very excited to be installing Scipion v3.0.5 at a new job - it has > been a while since I used Scipion and very many programs and features have > been added, it looks wonderful. > > One feature I would really like to use in Scipion is accurate CTF > estimation for particles on tilted micrographs. > As far as I know the options are patch-based CTF in gCTF (initially, > before particle picking), per-particle in gCTF, geometry aware CTF in > goCTF, and something similar in Warp. Maybe there are other options that > I’m not aware of - I’d be happy to hear about them! > > It looks like local or per-particle CTF are not available with gCTF in > Scipion3 - is that right? > > Using the plugin manager I installed gctf-1.18 > Then, since the github page mentions 1.18 is specifically for phase plate, > I installed gctf-1.06 with the plugin manager - but the ProtGctf protocol > in Scipion is not changed and still has no options relating to patch or > per-particle CTF. > > So, can I get accurate particle defocus values from tilted data in a > Scipion workflow? > > Many thanks, > Teige > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Matthews-Palmer, T. <t.m...@im...> - 2020-11-06 06:54:46
|
Dear Scipion users & devs, I’m very excited to be installing Scipion v3.0.5 at a new job - it has been a while since I used Scipion and very many programs and features have been added, it looks wonderful. One feature I would really like to use in Scipion is accurate CTF estimation for particles on tilted micrographs. As far as I know the options are patch-based CTF in gCTF (initially, before particle picking), per-particle in gCTF, geometry aware CTF in goCTF, and something similar in Warp. Maybe there are other options that I’m not aware of - I’d be happy to hear about them! It looks like local or per-particle CTF are not available with gCTF in Scipion3 - is that right? Using the plugin manager I installed gctf-1.18 Then, since the github page mentions 1.18 is specifically for phase plate, I installed gctf-1.06 with the plugin manager - but the ProtGctf protocol in Scipion is not changed and still has no options relating to patch or per-particle CTF. So, can I get accurate particle defocus values from tilted data in a Scipion workflow? Many thanks, Teige |
|
From: Tetter S. <tet...@or...> - 2020-10-30 08:50:01
|
I can't locate any file named xmipp.conf actually, not here nor anywhere else.
##
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ ls
CHANGELOG.md LICENSE README.md scripts src xmipp
##
Stephan
________________________________
Von: Pablo Conesa <pc...@cn...>
Gesendet: Freitag, 30. Oktober 2020 09:27:27
An: sci...@li...
Betreff: Re: [scipion-users] Installation trouble
What is the content of :
~/tetterst/software/em/xmippSrc-v3.20.07/xmipp.conf ?
On 30/10/20 8:45, Tetter Stephan wrote:
I get the exact same error message again...
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$<mailto:hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$> sudo chmod +x xmipp
(.scipion3env) hilvertg@bamf ~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
Any other ideas?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...><mailto:sha...@gm...>
Gesendet: Donnerstag, 29. Oktober 2020 18:22:42
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
What if you download https://raw.githubusercontent.com/I2PC/xmipp/v3.20.07-Boreas/xmipp file into this folder and replace the old one (make it executable as well) and then try again step 4, does it still fail?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Thu, Oct 29, 2020 at 3:27 PM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear Grigory,
Step 4 does indeed cause trouble:
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$<mailto:hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$> ./xmipp config
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
What does that mean?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>>
Gesendet: Mittwoch, 28. Oktober 2020 10:38:04
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
Hi Tetter,
Could you try the following steps manually:
1) conda activate .scipion3env
2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
3) rm -f xmipp.conf
4) ./xmipp config
5) ./xmipp check_config
6) ./xmipp compileAndInstall N=4
7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp
If you have errors in step 4, please post it here.
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear all,
I am trying to install Scipion for single particle analysis, and more specifically for symmetry relaxation. Unfortunately I can't seem to get the installation to work. I am working with Ubuntu 16.04. Please be aware that I am not a well-versed Ubuntu user.
I have tried installation both via the conda version and the virtualenv version described on https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, but they both fail eventually. (I have changed the export PATH line to point to sr/local/cuda-9.0/bin to fit my setup.)
Below is what happens. Any ideas?
Thanks,
Stephan
hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libtiff5-dev' instead of 'libtiff-dev'
g++ is already the newest version (4:5.3.1-1ubuntu1).
gcc is already the newest version (4:5.3.1-1ubuntu1).
libfftw3-dev is already the newest version (3.3.4-2ubuntu1).
libjpeg-dev is already the newest version (8c-2ubuntu8).
make is already the newest version (4.1-6).
python3-tk is already the newest version (3.5.1-1).
libopenmpi-dev is already the newest version (1.10.2-8ubuntu1).
libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5).
libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7).
openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04).
libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1).
0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin
hilvertg@bamf:~$ python -m pip install --user scipion-installerRequirement already satisfied: scipion-installer in ./.local/lib/python2.7/site-packages (1.0.9)
Requirement already satisfied: virtualenv in ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0)
Requirement already satisfied: six<2,>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) (1.10.0)
Requirement already satisfied: appdirs<2,>=1.4.3 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (1.4.4)
Requirement already satisfied: distlib<1,>=0.3.1 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (0.3.1)
Requirement already satisfied: importlib-resources>=1.0; python_version < "3.7" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.2.0)
Requirement already satisfied: importlib-metadata<3,>=0.12; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.0.0)
Requirement already satisfied: filelock<4,>=3.0.0 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.0.12)
Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.3.5)
Requirement already satisfied: typing; python_version < "3.5" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3)
Requirement already satisfied: contextlib2; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1)
Requirement already satisfied: zipp>=0.4; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (1.2.0)
Requirement already satisfied: singledispatch; python_version < "3.4" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3)
Requirement already satisfied: configparser>=3.5; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; python_version < "3.8"->virtualenv->scipion-installer) (4.0.2)
Requirement already satisfied: scandir; python_version < "3.5" in /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32"->virtualenv->scipion-installer) (1.9.0)
hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created virtual environment CPython3.5.2.final.0-64 in 99ms
creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, clear=False, global=False)
seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv)
added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2, cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1, kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0, scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1, setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1
activators PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0)
Requirement already satisfied: requests<=2.23.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (2.23.0)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.11)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2)
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-app in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: outdated==0.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0)
Requirement already satisfied: scipion-em in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4)
Requirement already satisfied: littleutils in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (0.2.2)
Requirement already satisfied: requests in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (2.23.0)
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (3.0.5)
Requirement already satisfied: biopython==1.76 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (1.76)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.11)
Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.0.3)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (4.0.2)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (50.3.2)
Scipion v3.0.5 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Building scipion-em-xmipp ...
/home/hilvertg/tetterst/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7.1
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-em-xmipp==20.7.1 in ./.scipion3env/lib/python3.5/site-packages (20.7.1)
Requirement already satisfied: joblib in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.14.1)
Requirement already satisfied: peppercorn in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.6)
Requirement already satisfied: plotter in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (1.3.17)
Requirement already satisfied: scons in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (4.0.1)
Requirement already satisfied: scikit-learn==0.22.1 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.22.1)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from scons->scipion-em-xmipp==20.7.1) (50.3.2)
Requirement already satisfied: scipy>=0.17.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1)
Requirement already satisfied: numpy>=1.11.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4)
Done (0.36 seconds)
Building xmippSrc-3.20.07 ...
Skipping command: wget -nv -c -O /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz
mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz
All targets exist.
Skipping command: tar -xf xmippSrc-v3.20.07.tgz
All targets exist.
cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
Traceback (most recent call last):
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 453, in <module>
main()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 161, in execute
"running '%s')" % (t, cmd))
AssertionError: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Something went wrong running:
cd /home/hilvertg/tetterst &&
/usr/bin/python3 -m virtualenv --python=python3 .scipion3env &&
. /home/hilvertg/tetterst/.scipion3env/bin/activate &&
cd /home/hilvertg/tetterst &&
mkdir -p software/lib &&
mkdir -p software/bindings &&
mkdir -p software/em &&
export SCIPION_HOME=/home/hilvertg/tetterst &&
pip install scipion-pyworkflow &&
pip install scipion-app &&
python -m scipion installp -p scipion-em-xmipp -j 4
Installation cancelled.
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
|
|
From: Pablo C. <pc...@cn...> - 2020-10-30 08:27:42
|
What is the content of : ~/tetterst/software/em/xmippSrc-v3.20.07/xmipp.conf ? On 30/10/20 8:45, Tetter Stephan wrote: > I get the exact same error message again... > > (.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ > sudo chmod +x xmipp > (.scipion3env) hilvertg@bamf ~/tetterst/software/em/xmippSrc-v3.20.07$ > ./xmipp config > Traceback (most recent call last): > File "./xmipp", line 1753, in <module> > XMIPP_SCRIPT_VERSION = getScriptVersion() > File "./xmipp", line 1718, in getScriptVersion > return lastCommit[0].strip() > IndexError: list index out of range > > Any other ideas? > > Thanks, > > Stephan > > ------------------------------------------------------------------------ > *Von:* Grigory Sharov <sha...@gm...> > *Gesendet:* Donnerstag, 29. Oktober 2020 18:22:42 > *An:* Mailing list for Scipion users > *Betreff:* Re: [scipion-users] Installation trouble > What if you download > https://raw.githubusercontent.com/I2PC/xmipp/v3.20.07-Boreas/xmipp file > into this folder and replace the old one (make it executable as well) > and then try again step 4, does it still fail? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Oct 29, 2020 at 3:27 PM Tetter Stephan > <tet...@or... <mailto:tet...@or...>> wrote: > > Dear Grigory, > > Step 4 does indeed cause trouble: > > (.scipion3env) > hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config > Traceback (most recent call last): > File "./xmipp", line 1753, in <module> > XMIPP_SCRIPT_VERSION = getScriptVersion() > File "./xmipp", line 1718, in getScriptVersion > return lastCommit[0].strip() > IndexError: list index out of range > > What does that mean? > > Thanks, > Stephan > > > ------------------------------------------------------------------------ > *Von:* Grigory Sharov <sha...@gm... > <mailto:sha...@gm...>> > *Gesendet:* Mittwoch, 28. Oktober 2020 10:38:04 > *An:* Mailing list for Scipion users > *Betreff:* Re: [scipion-users] Installation trouble > Hi Tetter, > > Could you try the following steps manually: > > 1) conda activate .scipion3env > 2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 > 3) rm -f xmipp.conf > 4) ./xmipp config > 5) ./xmipp check_config > 6) ./xmipp compileAndInstall N=4 > 7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp > > If you have errors in step 4, please post it here. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan > <tet...@or... <mailto:tet...@or...>> wrote: > > Dear all, > > > I am trying to install Scipion for single particle analysis, > and more specifically for symmetry relaxation. Unfortunately I > can't seem to get the installation to work. I am working with > Ubuntu 16.04. Please be aware that I am not a well-versed > Ubuntu user. > > > I have tried installation both via the conda version and the > virtualenv version described on > https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, > but they both fail eventually. (I have changed the export PATH > line to point to sr/local/cuda-9.0/bin to fit my setup.) > > > Below is what happens. Any ideas? > > > Thanks, > > > Stephan > > > hilvertg@bamf:~$ sudo apt-get install gcc g++ make > libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev > libjpeg-dev libsqlite3-dev openjdk-8-jdk > Reading package lists... Done > Building dependency tree > Reading state information... Done > Note, selecting 'libtiff5-dev' instead of 'libtiff-dev' > g++ is already the newest version (4:5.3.1-1ubuntu1). > gcc is already the newest version (4:5.3.1-1ubuntu1). > libfftw3-dev is already the newest version (3.3.4-2ubuntu1). > libjpeg-dev is already the newest version (8c-2ubuntu8). > make is already the newest version (4.1-6). > python3-tk is already the newest version (3.5.1-1). > libopenmpi-dev is already the newest version (1.10.2-8ubuntu1). > libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5). > libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7). > openjdk-8-jdk is already the newest version > (8u272-b10-0ubuntu1~16.04). > libhdf5-dev is already the newest version > (1.8.16+docs-4ubuntu1.1). > 0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded. > > hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin > > > hilvertg@bamf:~$ python -m pip install --user > scipion-installerRequirement already satisfied: > scipion-installer in ./.local/lib/python2.7/site-packages (1.0.9) > Requirement already satisfied: virtualenv in > ./.local/lib/python2.7/site-packages (from scipion-installer) > (20.1.0) > Requirement already satisfied: six<2,>=1.9.0 in > /usr/local/lib/python2.7/dist-packages (from > virtualenv->scipion-installer) (1.10.0) > Requirement already satisfied: appdirs<2,>=1.4.3 in > ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (1.4.4) > Requirement already satisfied: distlib<1,>=0.3.1 in > ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (0.3.1) > Requirement already satisfied: importlib-resources>=1.0; > python_version < "3.7" in ./.local/lib/python2.7/site-packages > (from virtualenv->scipion-installer) (3.2.0) > Requirement already satisfied: importlib-metadata<3,>=0.12; > python_version < "3.8" in ./.local/lib/python2.7/site-packages > (from virtualenv->scipion-installer) (2.0.0) > Requirement already satisfied: filelock<4,>=3.0.0 in > ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (3.0.12) > Requirement already satisfied: pathlib2<3,>=2.3.3; > python_version < "3.4" and sys_platform != "win32" in > ./.local/lib/python2.7/site-packages (from > virtualenv->scipion-installer) (2.3.5) > Requirement already satisfied: typing; python_version < "3.5" > in ./.local/lib/python2.7/site-packages (from > importlib-resources>=1.0; python_version < > "3.7"->virtualenv->scipion-installer) (3.7.4.3) > Requirement already satisfied: contextlib2; python_version < > "3" in ./.local/lib/python2.7/site-packages (from > importlib-resources>=1.0; python_version < > "3.7"->virtualenv->scipion-installer) (0.6.0.post1) > Requirement already satisfied: zipp>=0.4; python_version < > "3.8" in ./.local/lib/python2.7/site-packages (from > importlib-resources>=1.0; python_version < > "3.7"->virtualenv->scipion-installer) (1.2.0) > Requirement already satisfied: singledispatch; python_version > < "3.4" in ./.local/lib/python2.7/site-packages (from > importlib-resources>=1.0; python_version < > "3.7"->virtualenv->scipion-installer) (3.4.0.3) > Requirement already satisfied: configparser>=3.5; > python_version < "3" in ./.local/lib/python2.7/site-packages > (from importlib-metadata<3,>=0.12; python_version < > "3.8"->virtualenv->scipion-installer) (4.0.2) > Requirement already satisfied: scandir; python_version < "3.5" > in /usr/local/lib/python2.7/dist-packages (from > pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != > "win32"->virtualenv->scipion-installer) (1.9.0) > > > hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv > -j 4created virtual environment CPython3.5.2.final.0-64 in 99ms > creator > CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, > clear=False, global=False) > seeder FromAppData(download=False, wheel=bundle, > setuptools=bundle, pip=bundle, via=copy, > app_data_dir=/home/hilvertg/.local/share/virtualenv) > added seed packages: Pillow==7.1.2, SCons==4.0.1, > bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, > chardet==3.0.4, configparser==4.0.2, cycler==0.10.0, > future==0.18.2, idna==2.10, joblib==0.14.1, kiwisolver==1.1.0, > littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, > outdated==0.2.0, peppercorn==0.6, pip==20.2.4, > plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, > python_dateutil==2.8.1, requests==2.23.0, > scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, > scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, > scipy==1.4.1, setuptools==50.3.2, six==1.15.0, > urllib3==1.25.11, wheel==0.35.1 > activators > PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator > DEPRECATION: Python 3.5 reached the end of its life on > September 13th, 2020. Please upgrade your Python as Python 3.5 > is no longer maintained. pip 21.0 will drop support for Python > 3.5 in January 2021. pip 21.0 will remove support for this > functionality. > Requirement already satisfied: scipion-pyworkflow in > ./.scipion3env/lib/python3.5/site-packages (3.0.5) > Requirement already satisfied: matplotlib<=3.2.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (3.0.3) > Requirement already satisfied: psutil<=5.7.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (5.7.0) > Requirement already satisfied: requests<=2.23.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (2.23.0) > Requirement already satisfied: numpy<=1.18.4 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (1.18.4) > Requirement already satisfied: pillow<=7.1.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (1.2.0) > Requirement already satisfied: configparser<=5.0.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow) (4.0.2) > Requirement already satisfied: cycler>=0.10 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (2020.6.20) > Requirement already satisfied: idna<3,>=2.5 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (2.10) > Requirement already satisfied: > urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (1.25.11) > Requirement already satisfied: chardet<4,>=3.0.2 in > ./.scipion3env/lib/python3.5/site-packages (from > requests<=2.23.0->scipion-pyworkflow) (3.0.4) > Requirement already satisfied: future>=0.16.0 in > ./.scipion3env/lib/python3.5/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) > Requirement already satisfied: six in > ./.scipion3env/lib/python3.5/site-packages (from > cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2) > DEPRECATION: Python 3.5 reached the end of its life on > September 13th, 2020. Please upgrade your Python as Python 3.5 > is no longer maintained. pip 21.0 will drop support for Python > 3.5 in January 2021. pip 21.0 will remove support for this > functionality. > Requirement already satisfied: scipion-app in > ./.scipion3env/lib/python3.5/site-packages (3.0.5) > Requirement already satisfied: outdated==0.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from scipion-app) > (0.2.0) > Requirement already satisfied: scipion-em in > ./.scipion3env/lib/python3.5/site-packages (from scipion-app) > (3.0.4) > Requirement already satisfied: littleutils in > ./.scipion3env/lib/python3.5/site-packages (from > outdated==0.2.0->scipion-app) (0.2.2) > Requirement already satisfied: requests in > ./.scipion3env/lib/python3.5/site-packages (from > outdated==0.2.0->scipion-app) (2.23.0) > Requirement already satisfied: scipion-pyworkflow in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em->scipion-app) (3.0.5) > Requirement already satisfied: biopython==1.76 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em->scipion-app) (1.76) > Requirement already satisfied: idna<3,>=2.5 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (2.10) > Requirement already satisfied: chardet<4,>=3.0.2 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (3.0.4) > Requirement already satisfied: certifi>=2017.4.17 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (2020.6.20) > Requirement already satisfied: > urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in > ./.scipion3env/lib/python3.5/site-packages (from > requests->outdated==0.2.0->scipion-app) (1.25.11) > Requirement already satisfied: matplotlib<=3.2.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (3.0.3) > Requirement already satisfied: configparser<=5.0.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (4.0.2) > Requirement already satisfied: numpy<=1.18.4 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) > Requirement already satisfied: pillow<=7.1.2 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: psutil<=5.7.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) > Requirement already satisfied: cycler>=0.10 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (0.10.0) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (2.8.1) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./.scipion3env/lib/python3.5/site-packages (from > matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (1.1.0) > Requirement already satisfied: future>=0.16.0 in > ./.scipion3env/lib/python3.5/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) > (0.18.2) > Requirement already satisfied: six in > ./.scipion3env/lib/python3.5/site-packages (from > cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (1.15.0) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) > (50.3.2) > Scipion v3.0.5 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in > Scipion plugin manager window) > > > Building scipion-em-xmipp ... > /home/hilvertg/tetterst/.scipion3env/bin/python -m pip install > scipion-em-xmipp==20.7.1 > DEPRECATION: Python 3.5 reached the end of its life on > September 13th, 2020. Please upgrade your Python as Python 3.5 > is no longer maintained. pip 21.0 will drop support for Python > 3.5 in January 2021. pip 21.0 will remove support for this > functionality. > Requirement already satisfied: scipion-em-xmipp==20.7.1 in > ./.scipion3env/lib/python3.5/site-packages (20.7.1) > Requirement already satisfied: joblib in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em-xmipp==20.7.1) (0.14.1) > Requirement already satisfied: peppercorn in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em-xmipp==20.7.1) (0.6) > Requirement already satisfied: plotter in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em-xmipp==20.7.1) (1.3.17) > Requirement already satisfied: scons in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em-xmipp==20.7.1) (4.0.1) > Requirement already satisfied: scikit-learn==0.22.1 in > ./.scipion3env/lib/python3.5/site-packages (from > scipion-em-xmipp==20.7.1) (0.22.1) > Requirement already satisfied: setuptools in > ./.scipion3env/lib/python3.5/site-packages (from > scons->scipion-em-xmipp==20.7.1) (50.3.2) > Requirement already satisfied: scipy>=0.17.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1) > Requirement already satisfied: numpy>=1.11.0 in > ./.scipion3env/lib/python3.5/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4) > Done (0.36 seconds) > Building xmippSrc-3.20.07 ... > Skipping command: wget -nv -c -O > /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz > mv -v > /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part > /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07.tgz > All targets exist. > cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 > cd . && ./xmipp config noAsk && ./xmipp check_config && > ./xmipp compileAndInstall N=4 && ln -srfn build > /home/hilvertg/tetterst/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > Traceback (most recent call last): > File "./xmipp", line 1753, in <module> > XMIPP_SCRIPT_VERSION = getScriptVersion() > File "./xmipp", line 1718, in getScriptVersion > return lastCommit[0].strip() > IndexError: list index out of range > Traceback (most recent call last): > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", > line 453, in <module> > main() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", > line 296, in main > installPluginMethods() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", > line 231, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 220, in execute > command.execute() > File > "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", > line 161, in execute > "running '%s')" % (t, cmd)) > AssertionError: target > '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln > -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - > && touch installation_finished && rm bindings_linked 2> > /dev/null') > Error at main: target > '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln > -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - > && touch installation_finished && rm bindings_linked 2> > /dev/null') > > Something went wrong running: > cd /home/hilvertg/tetterst && > /usr/bin/python3 -m virtualenv --python=python3 .scipion3env && > . /home/hilvertg/tetterst/.scipion3env/bin/activate && > cd /home/hilvertg/tetterst && > mkdir -p software/lib && > mkdir -p software/bindings && > mkdir -p software/em && > export SCIPION_HOME=/home/hilvertg/tetterst && > pip install scipion-pyworkflow && > pip install scipion-app && > python -m scipion installp -p scipion-em-xmipp -j 4 > Installation cancelled. > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Tetter S. <tet...@or...> - 2020-10-30 07:45:51
|
I get the exact same error message again...
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ sudo chmod +x xmipp
(.scipion3env) hilvertg@bamf ~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
Any other ideas?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...>
Gesendet: Donnerstag, 29. Oktober 2020 18:22:42
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
What if you download https://raw.githubusercontent.com/I2PC/xmipp/v3.20.07-Boreas/xmipp file into this folder and replace the old one (make it executable as well) and then try again step 4, does it still fail?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Thu, Oct 29, 2020 at 3:27 PM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear Grigory,
Step 4 does indeed cause trouble:
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
What does that mean?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>>
Gesendet: Mittwoch, 28. Oktober 2020 10:38:04
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
Hi Tetter,
Could you try the following steps manually:
1) conda activate .scipion3env
2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
3) rm -f xmipp.conf
4) ./xmipp config
5) ./xmipp check_config
6) ./xmipp compileAndInstall N=4
7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp
If you have errors in step 4, please post it here.
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear all,
I am trying to install Scipion for single particle analysis, and more specifically for symmetry relaxation. Unfortunately I can't seem to get the installation to work. I am working with Ubuntu 16.04. Please be aware that I am not a well-versed Ubuntu user.
I have tried installation both via the conda version and the virtualenv version described on https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, but they both fail eventually. (I have changed the export PATH line to point to sr/local/cuda-9.0/bin to fit my setup.)
Below is what happens. Any ideas?
Thanks,
Stephan
hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libtiff5-dev' instead of 'libtiff-dev'
g++ is already the newest version (4:5.3.1-1ubuntu1).
gcc is already the newest version (4:5.3.1-1ubuntu1).
libfftw3-dev is already the newest version (3.3.4-2ubuntu1).
libjpeg-dev is already the newest version (8c-2ubuntu8).
make is already the newest version (4.1-6).
python3-tk is already the newest version (3.5.1-1).
libopenmpi-dev is already the newest version (1.10.2-8ubuntu1).
libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5).
libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7).
openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04).
libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1).
0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin
hilvertg@bamf:~$ python -m pip install --user scipion-installerRequirement already satisfied: scipion-installer in ./.local/lib/python2.7/site-packages (1.0.9)
Requirement already satisfied: virtualenv in ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0)
Requirement already satisfied: six<2,>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) (1.10.0)
Requirement already satisfied: appdirs<2,>=1.4.3 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (1.4.4)
Requirement already satisfied: distlib<1,>=0.3.1 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (0.3.1)
Requirement already satisfied: importlib-resources>=1.0; python_version < "3.7" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.2.0)
Requirement already satisfied: importlib-metadata<3,>=0.12; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.0.0)
Requirement already satisfied: filelock<4,>=3.0.0 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.0.12)
Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.3.5)
Requirement already satisfied: typing; python_version < "3.5" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3)
Requirement already satisfied: contextlib2; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1)
Requirement already satisfied: zipp>=0.4; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (1.2.0)
Requirement already satisfied: singledispatch; python_version < "3.4" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3)
Requirement already satisfied: configparser>=3.5; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; python_version < "3.8"->virtualenv->scipion-installer) (4.0.2)
Requirement already satisfied: scandir; python_version < "3.5" in /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32"->virtualenv->scipion-installer) (1.9.0)
hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created virtual environment CPython3.5.2.final.0-64 in 99ms
creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, clear=False, global=False)
seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv)
added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2, cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1, kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0, scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1, setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1
activators PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0)
Requirement already satisfied: requests<=2.23.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (2.23.0)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.11)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2)
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-app in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: outdated==0.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0)
Requirement already satisfied: scipion-em in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4)
Requirement already satisfied: littleutils in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (0.2.2)
Requirement already satisfied: requests in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (2.23.0)
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (3.0.5)
Requirement already satisfied: biopython==1.76 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (1.76)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.11)
Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.0.3)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (4.0.2)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (50.3.2)
Scipion v3.0.5 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Building scipion-em-xmipp ...
/home/hilvertg/tetterst/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7.1
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-em-xmipp==20.7.1 in ./.scipion3env/lib/python3.5/site-packages (20.7.1)
Requirement already satisfied: joblib in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.14.1)
Requirement already satisfied: peppercorn in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.6)
Requirement already satisfied: plotter in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (1.3.17)
Requirement already satisfied: scons in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (4.0.1)
Requirement already satisfied: scikit-learn==0.22.1 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.22.1)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from scons->scipion-em-xmipp==20.7.1) (50.3.2)
Requirement already satisfied: scipy>=0.17.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1)
Requirement already satisfied: numpy>=1.11.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4)
Done (0.36 seconds)
Building xmippSrc-3.20.07 ...
Skipping command: wget -nv -c -O /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz
mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz
All targets exist.
Skipping command: tar -xf xmippSrc-v3.20.07.tgz
All targets exist.
cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
Traceback (most recent call last):
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 453, in <module>
main()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 161, in execute
"running '%s')" % (t, cmd))
AssertionError: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Something went wrong running:
cd /home/hilvertg/tetterst &&
/usr/bin/python3 -m virtualenv --python=python3 .scipion3env &&
. /home/hilvertg/tetterst/.scipion3env/bin/activate &&
cd /home/hilvertg/tetterst &&
mkdir -p software/lib &&
mkdir -p software/bindings &&
mkdir -p software/em &&
export SCIPION_HOME=/home/hilvertg/tetterst &&
pip install scipion-pyworkflow &&
pip install scipion-app &&
python -m scipion installp -p scipion-em-xmipp -j 4
Installation cancelled.
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scipion-users mailing list
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From: Moustafa, I. M. <ri...@ps...> - 2020-10-29 22:26:05
|
It seems working, at least I can launch the gui. I am going through the localrec tutorial from scipion page and will let you know if I come through problems. Thank you for your help. Ibrahim ________________________________ From: pc...@cn... <pc...@cn...> Sent: Thursday, October 29, 2020 2:44 PM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] problem installing scipion3 I don't see any suspicious value. I understand, apart from not understanding the location of localrec, all seems to work? El 29 oct. 2020 17:47, "Moustafa, Ibrahim M." <ri...@ps...> escribió: Many thanks David! downgrading numpy to version 1.18.4 solved the issue. Now Scipion3 can launch the gui. Pablo: I see localrec indicated as installed plugin in the plugins manager. Still puzzled why it did not build in the site-packages under .scipionenv directory! Not sure if that affects localrec or it can still work properly. The output of scipion3 printenv is shown below. If it needs edit please let me know! Scipion v3.0.5 () devel export CUDA_BIN="/opt/debian10/cuda/10.1.243/bin" export CUDA_LIB="/opt/debian10/cuda/10.1.243/lib64" export EMAN2_HOME="/usr/local/scipion/software/em/eman-2.31" export EMFACILITIES_HOME="/usr/local/scipion" export EM_ROOT="software/em" export LOCSCALE_HOME="/usr/local/scipion/software/em/locscale-0.1" export MAXIT_HOME="/usr/local/scipion/software/em/maxit-10.1" export OPENCV="False" export RELION_HOME="/usr/local/scipion/software/em/relion-3.1.0" export SCIPION_CONFIG="/usr/local/scipion/config/scipion.conf" export SCIPION_CWD="/home/ria2" export SCIPION_DOMAIN="pwem" export SCIPION_FONT_NAME="Helvetica" export SCIPION_HOME="/usr/local/scipion" export SCIPION_HOSTS="/usr/local/scipion/config/hosts.conf" export SCIPION_LOCAL_CONFIG="/home/ria2/.config/scipion/scipion.conf" export SCIPION_LOG="/storage/ria2/ScipionUserData/logs/scipion.log" export SCIPION_LOGO="scipion_logo.gif" export SCIPION_LOGS="/storage/ria2/ScipionUserData/logs" export SCIPION_NOTES_ARGS="" export SCIPION_NOTES_FILE="notes.txt" export SCIPION_NOTES_PROGRAM="" export SCIPION_NOTIFY="False" export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/" export SCIPION_PROTOCOLS="/usr/local/scipion/config/protocols.conf" export SCIPION_SOFTWARE="/usr/local/scipion/software" export SCIPION_SUPPORT_EMAIL="sc...@cn..." export SCIPION_TESTS="/usr/local/scipion/data/tests" export SCIPION_TESTS_CMD="scipion3 tests" export SCIPION_TESTS_OUTPUT="/usr/local/scipion/Tests" export SCIPION_TMP="/storage/ria2/ScipionUserData/tmp" export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion" export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software" export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests" export SCIPION_USER_DATA="/storage/ria2/ScipionUserData" export SCIPION_VERSION="v3.0.5 () devel" export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]" export XMIPP2_HOME="/usr/local/scipion/software/em/Xmipp-2.4-src" export XMIPP_HOME="/usr/local/scipion/software/em/xmipp" Thanks, Ibrahim ________________________________ From: David Maluenda <dma...@cn...> Sent: Thursday, October 29, 2020 6:48 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] problem installing scipion3 The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by ./scipion3 python -m pip install numpy==1.18.4 Hope it helps, Regards, <http://ucm.es/> _____ Dr. David Maluenda Niubó dma...@cn...<mailto:dma...@cn...> - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología<http://www.cnb.csic.es/> BioComputing Unit<http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote: I think now localrec is installed depite the error message and xmipp looks fixed too. Could you please send the output of: scipion3 printenv On 29/10/20 4:18, Moustafa, Ibrahim M. wrote: Hi David, I appreciate your help. I tried what you suggested, removed xmipp and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It compiled with no error. I re-installed scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error: Successfully installed scipion-em-localrec-3.0.1 Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> main() File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main installPluginMethods() File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods installed = plugin.installPipModule(version=pluginVersion) File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule environment.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute command.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1') Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1') No idea why it could not build in the site-packages directory (which I own)! Now if I run: 'scipion3 inspect localrec' I get the following: Scipion v3.0.5 () devel Plugin: localrec >>> constants: loaded >>> convert: loaded >>> protocols: loaded >>> wizards: missing >>> viewers: loaded >>> tests: loaded I also still not able to run Scipion3, I get the following error: Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> main() File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main ProjectManagerWindow().show() File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__ ProjectBaseWindow.__init__(self, title, minsize=(750, 500), File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__ Window.__init__(self, title, masterWindow, weight=weight, File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__ pw.Config.getDomain()._discoverGUIPlugins() File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins entry_point.load() File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load self.require(*args, **kwargs) File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require items = working_set.resolve(reqs, env, installer, extras=self.extras) File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'}) Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'}) Any suggestion to get this fixed is appreciated! Thanks, Ibrahim ________________________________ From: David Maluenda <dma...@cn...><mailto:dma...@cn...> Sent: Wednesday, October 28, 2020 2:32 PM To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...> Subject: Re: [scipion-users] problem installing scipion3 Hi, The error depicted above sounds me. I think it's raised when the xmipp plugin version is not sync with the xmipp software version. Please, try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8' Hope it helps. Regards, _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub...<mailto:dma...@ub...> Wavefront Engineering Group Applied Physics (UB) El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> escribió: Running "scipion3 inspect localrec" gives the following error: Scipion v3.0.5 () devel >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Plugin: localrec >>> constants: loaded >>> convert: loaded >>> protocols: loaded >>> wizards: missing >>> viewers: loaded >>> tests: error -> Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule m = importlib.import_module('%s.%s' % (name, subname)) File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1014, in _gcd_import File "<frozen importlib._bootstrap>", line 991, in _find_and_load File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 671, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 783, in exec_module File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module> from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase, File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module> from xmipp3.protocols import XmippProtCreateMask3D File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module> from .protocol_ctf_micrographs import XmippProtCTFMicrographs File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module> from xmipp3.base import isMdEmpty ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py) Ibrahim ________________________________ From: Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> Sent: Wednesday, October 28, 2020 2:23 AM To: sci...@li...<mailto:sci...@li...> <sci...@li...<mailto:sci...@li...>> Subject: Re: [scipion-users] problem installing scipion3 Despite the error, it seems localrec is installed. What about: ./scipion3 inspect localrec On 27/10/20 19:12, Moustafa, Ibrahim M. wrote: scipion-em-localrec 3.0.1 -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: David M. <dma...@cn...> - 2020-10-29 21:04:48
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Hi, Please check https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration for a more detailed information about how to set and edit compiling flags in Xmipp. Regards, _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub... Wavefront Engineering Group Applied Physics (UB) El jue., 29 oct. 2020 16:21, David <dst...@cn...> escribió: > Hi, > > > other option is to set these directly in the xmipp.conf file (located in > your xmipp install folder, typically 'xmipp-bundle'), and then recompile > xmipp (typically 'scipion3 run path_to_xmipp_script_in_xmipp-bundle'). > > The problem is gonna be our default optimization flags (-mtune=native > -march=native). It should be enough to remove them. > > > KR, > > David S. > > > On 29/10/20 16:11, Carlos Oscar Sorzano wrote: > > Dear Wolfgang, > > in the compilation of Xmipp, you can set the environment variable CXXFLAGS > before calling the xmipp script. From the Scipion installation I am not > sure how to pass it to the xmipp script. It may be that setting it in the > shell before calling scipion suffices. But I have never tried. > > Kind regards, Carlos Oscar > El 29/10/2020 a las 11:13, Pablo Conesa escribió: > > ? > > > -------- Forwarded Message -------- > Subject: [scipion-users] scipion-installer - how do i change compiler > optimization flags? > Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) > From: Lugmayr, Wolfgang <w.l...@uk...> <w.l...@uk...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > <sci...@li...> > To: Mailing list for Scipion users <sci...@li...> > <sci...@li...> > > hi, > > i installed and compiled scipion 3.0.5-devel on a system with intel cpus. > > when i run now scipion on new nodes with "AMD EPYC 7402" processors the > executable fails with: > $ scipion3 last Scipion v3.0.5 () devel > sh: line 1: 45875 Illegal instruction python -m scipion last > > so i do not want to have 2 versions of scipion3 but maybe compile it with > intel and amd compatibility flags. > how do i set these flags? > > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Deutsches Elektronen-Synchrotron (DESY) > Notkestrasse 85 Gebäude 15 > 22607 Hamburg, Germany > Tel.: +49 40 8998-87652 > Email: wol...@cs...http://www.cssb-hamburg.de/ > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dieter B. <die...@me...> - 2020-10-29 19:53:53
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Dear Grigory, thanks a lot for the hint! It'll take time to install scipion first and get everything running but it is good to know that this is principally possible. I shall be happy to come back to you in the probable case of encountering problems :-). Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: die...@me... ------------------------------------------------------------------------ On 29.10.2020 20:34, Grigory Sharov wrote: > Hi Dieter, > > yes, it should be working from Scipion: scipion installp -p > scipion-em-cryodrgn > It does require relion plugin installed (but not relion binaries) > > Let me know if you have problems > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Oct 29, 2020 at 5:56 PM Dieter Blaas > <die...@me... <mailto:die...@me...>> > wrote: > > Hi, > > I'd like trying cryoDRGN on my dataset but had issues > installing it. > Is its installation supported within Scipion and if so, what do I > need > to do? > > Thanks, best, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail: die...@me... > <mailto:die...@me...> > ------------------------------------------------------------------------ > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-10-29 19:34:34
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Hi Dieter, yes, it should be working from Scipion: scipion installp -p scipion-em-cryodrgn It does require relion plugin installed (but not relion binaries) Let me know if you have problems Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Oct 29, 2020 at 5:56 PM Dieter Blaas <die...@me...> wrote: > Hi, > > I'd like trying cryoDRGN on my dataset but had issues installing it. > Is its installation supported within Scipion and if so, what do I need > to do? > > Thanks, best, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail: die...@me... > ------------------------------------------------------------------------ > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: <pc...@cn...> - 2020-10-29 18:45:39
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<div dir='auto'>I don't see any suspicious value.<div dir="auto"><br></div><div dir="auto">I understand, apart from not understanding the location of localrec, all seems to work?</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 29 oct. 2020 17:47, "Moustafa, Ibrahim M." <ri...@ps...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Many thanks David! downgrading numpy to version 1.18.4 solved the issue. Now Scipion3 can launch the gui.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Pablo: I see localrec indicated as installed plugin in the plugins manager. Still puzzled why it did not build in the site-packages under .scipionenv directory! Not sure if that affects localrec or it can still work properly.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> The output of scipion3 printenv is shown below. If it needs edit please let me know!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>export CUDA_BIN="/opt/debian10/cuda/10.1.243/bin"</div> <div>export CUDA_LIB="/opt/debian10/cuda/10.1.243/lib64"</div> <div>export EMAN2_HOME="/usr/local/scipion/software/em/eman-2.31"</div> <div>export EMFACILITIES_HOME="/usr/local/scipion"</div> <div>export EM_ROOT="software/em"</div> <div>export LOCSCALE_HOME="/usr/local/scipion/software/em/locscale-0.1"</div> <div>export MAXIT_HOME="/usr/local/scipion/software/em/maxit-10.1"</div> <div>export OPENCV="False"</div> <div>export RELION_HOME="/usr/local/scipion/software/em/relion-3.1.0"</div> <div>export SCIPION_CONFIG="/usr/local/scipion/config/scipion.conf"</div> <div>export SCIPION_CWD="/home/ria2"</div> <div>export SCIPION_DOMAIN="pwem"</div> <div>export SCIPION_FONT_NAME="Helvetica"</div> <div>export SCIPION_HOME="/usr/local/scipion"</div> <div>export SCIPION_HOSTS="/usr/local/scipion/config/hosts.conf"</div> <div>export SCIPION_LOCAL_CONFIG="/home/ria2/.config/scipion/scipion.conf"</div> <div>export SCIPION_LOG="/storage/ria2/ScipionUserData/logs/scipion.log"</div> <div>export SCIPION_LOGO="scipion_logo.gif"</div> <div>export SCIPION_LOGS="/storage/ria2/ScipionUserData/logs"</div> <div>export SCIPION_NOTES_ARGS=""</div> <div>export SCIPION_NOTES_FILE="notes.txt"</div> <div>export SCIPION_NOTES_PROGRAM=""</div> <div>export SCIPION_NOTIFY="False"</div> <div>export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"</div> export SCIPION_PROTOCOLS="/usr/local/scipion/config/protocols.conf"<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> export SCIPION_SOFTWARE="/usr/local/scipion/software" <div>export SCIPION_SUPPORT_EMAIL="scipion@cnb.csic.es"</div> <div>export SCIPION_TESTS="/usr/local/scipion/data/tests"</div> <div>export SCIPION_TESTS_CMD="scipion3 tests"</div> <div>export SCIPION_TESTS_OUTPUT="/usr/local/scipion/Tests"</div> <div>export SCIPION_TMP="/storage/ria2/ScipionUserData/tmp"</div> <div>export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"</div> <div>export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"</div> <div>export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"</div> <div>export SCIPION_USER_DATA="/storage/ria2/ScipionUserData"</div> <div>export SCIPION_VERSION="v3.0.5 () devel"</div> <div>export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"</div> <div>export XMIPP2_HOME="/usr/local/scipion/software/em/Xmipp-2.4-src"</div> export XMIPP_HOME="/usr/local/scipion/software/em/xmipp"<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <div></div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> David Maluenda <dmaluenda@cnb.csic.es><br /> <b>Sent:</b> Thursday, October 29, 2020 6:48 AM<br /> <b>To:</b> Mailing list for Scipion users <scipion-users@lists.sourceforge.net><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="ltr"> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by</div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <blockquote style="margin:0 0 0 40px;border:none;padding:0px"> <div style="font-size:small;color:rgb( 0 , 0 , 0 )"><font face="monospace">./scipion3 python -m pip install numpy==1.18.4</font></div> </blockquote> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> Hope it helps,</div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> Regards,</div> <div> <div dir="ltr"> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div dir="ltr"> <div dir="ltr"><font color="#888888"></font></div> <div dir="ltr"><font color="#000000" face="trebuchet ms,sans-serif"> <div style="font-size:small;display:inline"><a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fucm.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004301017%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=85csE4HN%2BamymeYf96qZGBrQ9Lpe2TdyNiWtvzMyy7U%3D&reserved=0"></a></div> </font><font color="#000000" face="trebuchet ms,sans-serif"><b>_____<br /> Dr. David Maluenda Niubó</b><br /> </font></div> <div dir="ltr"><font color="#000000" face="trebuchet ms,sans-serif"><a href="mailto:dmaluenda@cnb.csic.es">dmaluenda@cnb.csic.es</a> </font><font color="#000000" face="trebuchet ms,sans-serif">- <font size="1">(+34)</font> 619 029 310</font></div> <div><span style="font-family:'trebuchet ms' , sans-serif"><a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cnb.csic.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6kFNVSCUIjY9yH8KWZdNRtX2stnOT92uoobn3EWhseo%3D&reserved=0"><font color="#0000ff">CSIC - Centro Nacional de Biotecnología</font></a></span></div> <div><span style="font-family:'trebuchet ms' , sans-serif"><font color="#0000ff"><a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiocomputingunit.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4PytI0mGWheRX0qMHZc1runOa3ipTB5axLBZ6bZMwjs%3D&reserved=0">BioComputing Unit</a><br /> </font></span></div> <div><font size="1" color="#cccccc" face="Arial"><br /> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration.</font></div> <div><font size="1" color="#cccccc" face="Arial"><br /> </font></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <br /> </div> <br /> <div> <div dir="ltr">On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>> wrote:<br /> </div> <blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"> <div> <p>I think now localrec is installed depite the error message and xmipp looks fixed too.</p> <p><br /> </p> <p>Could you please send the output of:</p> <p><br /> </p> <p>scipion3 printenv</p> <p><br /> </p> <p><br /> </p> <div>On 29/10/20 4:18, Moustafa, Ibrahim M. wrote:<br /> </div> <blockquote> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Hi David,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> I appreciate your help. I tried what you suggested, removed xmipp and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It compiled with no error. </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> I re-installed scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <pre style="margin:4px 0px;padding:8px;font-size:12px;line-height:1.50001;white-space:pre-wrap;border-radius:4px;color:rgb( 209 , 210 , 211 );text-align:left;font-family:'monaco' , 'menlo' , 'consolas' , 'courier new' , monospace"><span style="color:rgb( 0 , 0 , 0 )">Successfully installed scipion-em-localrec-3.0.1</span> <span style="color:rgb( 0 , 0 , 0 )">Traceback (most recent call last):</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></span> <span style="color:rgb( 0 , 0 , 0 )"> main()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main</span> <span style="color:rgb( 0 , 0 , 0 )"> installPluginMethods()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods</span> <span style="color:rgb( 0 , 0 , 0 )"> installed = plugin.installPipModule(version=pluginVersion)</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</span> <span style="color:rgb( 0 , 0 , 0 )"> environment.execute()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> self._executeTargets(targetList)</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</span> <span style="color:rgb( 0 , 0 , 0 )"> tgt.execute()</span> <span style="color:rgb( 0 , 0 , 0 )">File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> command.execute()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> assert glob(t), ("target '%s' not built (after "</span> <span style="color:rgb( 0 , 0 , 0 )">AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')</span> <span style="color:rgb( 0 , 0 , 0 )">Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')</span></pre> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> No idea why it could not build in the site-packages directory (which I own)!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Now if I run: 'scipion3 inspect localrec' I get the following: </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>Plugin: localrec</div> <div> >>> constants: loaded</div> <div> >>> convert: loaded</div> <div> >>> protocols: loaded</div> <div> >>> wizards: missing</div> <div> >>> viewers: loaded</div> <div> >>> tests: loaded</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> I also still not able to run Scipion3, I get the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Traceback (most recent call last): <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></div> <div> main()</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main</div> <div> ProjectManagerWindow().show()</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__</div> <div> ProjectBaseWindow.__init__(self, title, minsize=(750, 500),</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__</div> <div> Window.__init__(self, title, masterWindow, weight=weight,</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__</div> <div> pw.Config.getDomain()._discoverGUIPlugins()</div> <div> File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins</div> <div> entry_point.load()</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load</div> <div> self.require(*args, **kwargs)</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require</div> <div> items = working_set.resolve(reqs, env, installer, extras=self.extras)</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve</div> <div> raise VersionConflict(dist, req).with_context(dependent_req)</div> <div>pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})</div> <div>Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})</div> <br /> <br /> Any suggestion to get this fixed is appreciated!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim<br /> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> David Maluenda <a href="mailto:dmaluenda@cnb.csic.es"><dmaluenda@cnb.csic.es></a><br /> <b>Sent:</b> Wednesday, October 28, 2020 2:32 PM<br /> <b>To:</b> Mailing list for Scipion users <a href="mailto:scipion-users@lists.sourceforge.net"> <scipion-users@lists.sourceforge.net></a><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="auto">Hi, <div dir="auto"><br /> </div> <div dir="auto">The error depicted above sounds me. I think it's raised when the xmipp plugin version is not sync with the xmipp software version. Please, try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8'</div> <div dir="auto"><br /> </div> <div dir="auto"><br /> </div> <div dir="auto">Hope it helps.</div> <div dir="auto"><br /> </div> <div dir="auto">Regards,<br /> <br /> <div dir="auto">_____<br /> Dr. David Maluenda Niubó<br /> (+34) 619.029.310 - <a href="mailto:dmaluenda@ub.edu">dmaluenda@ub.edu</a><br /> Wavefront Engineering Group<br /> Applied Physics (UB)</div> </div> </div> <br /> <div> <div dir="ltr">El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <<a href="mailto:ria2@psu.edu">ria2@psu.edu</a>> escribió:<br /> </div> <blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"> <div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Running "scipion3 inspect localrec" gives the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div><br /> </div> <div> >>> WARNING: Image library not found!</div> <div> > Please install Xmipp to get full functionality.</div> <div>(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)</div> <div><br /> </div> <div><br /> </div> <div>Plugin: localrec</div> <div> >>> constants: loaded</div> <div> >>> convert: loaded</div> <div> >>> protocols: loaded</div> <div> >>> wizards: missing</div> <div> >>> viewers: loaded</div> <div> >>> tests: error -> Traceback (most recent call last):</div> <div> File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule</div> <div> m = importlib.import_module('%s.%s' % (name, subname))</div> <div> File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module</div> <div> return _bootstrap._gcd_import(name[level:], package, level)</div> <div> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import</div> <div> File "<frozen importlib._bootstrap>", line 991, in _find_and_load</div> <div> File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked</div> <div> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked</div> <div> File "<frozen importlib._bootstrap_external>", line 783, in exec_module</div> <div> File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed</div> File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module><br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase, <div> File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module></div> <div> from xmipp3.protocols import XmippProtCreateMask3D</div> <div> File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module></div> <div> from .protocol_ctf_micrographs import XmippProtCTFMicrographs</div> <div> File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module></div> <div> from xmipp3.base import isMdEmpty</div> ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py)<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"> <font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>><br /> <b>Sent:</b> Wednesday, October 28, 2020 2:23 AM<br /> <b>To:</b> <a href="mailto:scipion-users@lists.sourceforge.net"> scipion-users@lists.sourceforge.net</a> <<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a>><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <p>Despite the error, it seems localrec is installed.</p> <p>What about:</p> <p>./scipion3 inspect localrec</p> <p><br /> </p> <div>On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:<br /> </div> <blockquote>scipion-em-localrec 3.0.1</blockquote> <div>-- <br /> Pablo Conesa - <strong>Madrid <a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FjnNlurCxbneNXwp7bE3txsqZK8VC2JELVR%2Fvxl2FBc%3D&reserved=0"> Scipion</a> team</strong></div> </div> </div> _______________________________________________<br /> scipion-users mailing list<br /> <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br /> <a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004321001%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ygQiTpaQhhAPZskDNurYuAACI%2BM5mZ%2Fn8g%2FDuBss0yI%3D&reserved=0">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br /> </blockquote> </div> </div> <br /> <fieldset></fieldset> <br /> <fieldset></fieldset> <pre>_______________________________________________ scipion-users mailing list <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a> <a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004330999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=cKPih6fvBenoVP0i36Y7FHkkS2zCssv3GhWgehsI8%2BA%3D&reserved=0">https://lists.sourceforge.net/lists/listinfo/scipion-users</a> </pre> </blockquote> <div>-- <br /> Pablo Conesa - <strong>Madrid <a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004330999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=0wiCQk7AJ%2BYI12ia1td%2F9JOkXWNyF8IaRaSiSpVWXxI%3D&reserved=0"> Scipion</a> team</strong></div> </div> _______________________________________________<br /> scipion-users mailing list<br /> <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br /> <a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004340993%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rQsW3fVv1XKn6tJYefhAzJGiawp2dWzxejIw5ZhhUaw%3D&reserved=0">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br /> </blockquote> </div> </div> </div> </blockquote></div><br></div> |
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From: Dieter B. <die...@me...> - 2020-10-29 17:56:33
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Hi, I'd like trying cryoDRGN on my dataset but had issues installing it. Is its installation supported within Scipion and if so, what do I need to do? Thanks, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: die...@me... ------------------------------------------------------------------------ |
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From: Grigory S. <sha...@gm...> - 2020-10-29 17:23:21
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What if you download https://raw.githubusercontent.com/I2PC/xmipp/v3.20.07-Boreas/xmipp file into this folder and replace the old one (make it executable as well) and then try again step 4, does it still fail? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Oct 29, 2020 at 3:27 PM Tetter Stephan <tet...@or...> wrote: > Dear Grigory, > > Step 4 does indeed cause trouble: > > (.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ > ./xmipp config > Traceback (most recent call last): > File "./xmipp", line 1753, in <module> > XMIPP_SCRIPT_VERSION = getScriptVersion() > File "./xmipp", line 1718, in getScriptVersion > return lastCommit[0].strip() > IndexError: list index out of range > > What does that mean? > > Thanks, > Stephan > > > ------------------------------ > *Von:* Grigory Sharov <sha...@gm...> > *Gesendet:* Mittwoch, 28. Oktober 2020 10:38:04 > *An:* Mailing list for Scipion users > *Betreff:* Re: [scipion-users] Installation trouble > > Hi Tetter, > > Could you try the following steps manually: > > 1) conda activate .scipion3env > 2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 > 3) rm -f xmipp.conf > 4) ./xmipp config > 5) ./xmipp check_config > 6) ./xmipp compileAndInstall N=4 > 7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp > > If you have errors in step 4, please post it here. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...> > wrote: > >> Dear all, >> >> >> I am trying to install Scipion for single particle analysis, and more >> specifically for symmetry relaxation. Unfortunately I can't seem to get the >> installation to work. I am working with Ubuntu 16.04. Please be aware that >> I am not a well-versed Ubuntu user. >> >> >> I have tried installation both via the conda version and the virtualenv >> version described on >> https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, >> but they both fail eventually. (I have changed the export PATH line to >> point to sr/local/cuda-9.0/bin to fit my setup.) >> >> >> Below is what happens. Any ideas? >> >> >> Thanks, >> >> >> Stephan >> >> >> hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev >> python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev >> openjdk-8-jdk >> Reading package lists... Done >> Building dependency tree >> Reading state information... Done >> Note, selecting 'libtiff5-dev' instead of 'libtiff-dev' >> g++ is already the newest version (4:5.3.1-1ubuntu1). >> gcc is already the newest version (4:5.3.1-1ubuntu1). >> libfftw3-dev is already the newest version (3.3.4-2ubuntu1). >> libjpeg-dev is already the newest version (8c-2ubuntu8). >> make is already the newest version (4.1-6). >> python3-tk is already the newest version (3.5.1-1). >> libopenmpi-dev is already the newest version (1.10.2-8ubuntu1). >> libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5). >> libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7). >> openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04). >> libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1). >> 0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded. >> >> hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin >> >> >> hilvertg@bamf:~$ python -m pip install --user >> scipion-installerRequirement already satisfied: scipion-installer in >> ./.local/lib/python2.7/site-packages (1.0.9) >> Requirement already satisfied: virtualenv in >> ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0) >> Requirement already satisfied: six<2,>=1.9.0 in >> /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) >> (1.10.0) >> Requirement already satisfied: appdirs<2,>=1.4.3 in >> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) >> (1.4.4) >> Requirement already satisfied: distlib<1,>=0.3.1 in >> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) >> (0.3.1) >> Requirement already satisfied: importlib-resources>=1.0; python_version < >> "3.7" in ./.local/lib/python2.7/site-packages (from >> virtualenv->scipion-installer) (3.2.0) >> Requirement already satisfied: importlib-metadata<3,>=0.12; >> python_version < "3.8" in ./.local/lib/python2.7/site-packages (from >> virtualenv->scipion-installer) (2.0.0) >> Requirement already satisfied: filelock<4,>=3.0.0 in >> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) >> (3.0.12) >> Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" >> and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from >> virtualenv->scipion-installer) (2.3.5) >> Requirement already satisfied: typing; python_version < "3.5" in >> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; >> python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3) >> Requirement already satisfied: contextlib2; python_version < "3" in >> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; >> python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1) >> Requirement already satisfied: zipp>=0.4; python_version < "3.8" in >> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; >> python_version < "3.7"->virtualenv->scipion-installer) (1.2.0) >> Requirement already satisfied: singledispatch; python_version < "3.4" in >> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; >> python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3) >> Requirement already satisfied: configparser>=3.5; python_version < "3" in >> ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; >> python_version < "3.8"->virtualenv->scipion-installer) (4.0.2) >> Requirement already satisfied: scandir; python_version < "3.5" in >> /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; >> python_version < "3.4" and sys_platform != >> "win32"->virtualenv->scipion-installer) (1.9.0) >> >> >> hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j >> 4created virtual environment CPython3.5.2.final.0-64 in 99ms >> creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, >> clear=False, global=False) >> seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, >> pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv) >> added seed packages: Pillow==7.1.2, SCons==4.0.1, >> bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, chardet==3.0.4, >> configparser==4.0.2, cycler==0.10.0, future==0.18.2, idna==2.10, >> joblib==0.14.1, kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, >> numpy==1.18.4, outdated==0.2.0, peppercorn==0.6, pip==20.2.4, >> plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, >> requests==2.23.0, scikit_learn==0.22.1, scipion_app==3.0.5, >> scipion_em==3.0.4, scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, >> scipy==1.4.1, setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, >> wheel==0.35.1 >> activators >> PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator >> DEPRECATION: Python 3.5 reached the end of its life on September 13th, >> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip >> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove >> support for this functionality. >> Requirement already satisfied: scipion-pyworkflow in >> ./.scipion3env/lib/python3.5/site-packages (3.0.5) >> Requirement already satisfied: matplotlib<=3.2.2 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3) >> Requirement already satisfied: psutil<=5.7.0 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0) >> Requirement already satisfied: requests<=2.23.0 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) >> (2.23.0) >> Requirement already satisfied: numpy<=1.18.4 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) >> (1.18.4) >> Requirement already satisfied: pillow<=7.1.2 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2) >> Requirement already satisfied: bibtexparser<=1.2.0 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0) >> Requirement already satisfied: configparser<=5.0.0 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2) >> Requirement already satisfied: cycler>=0.10 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) >> Requirement already satisfied: python-dateutil>=2.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >> in ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) >> Requirement already satisfied: kiwisolver>=1.0.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0) >> Requirement already satisfied: certifi>=2017.4.17 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests<=2.23.0->scipion-pyworkflow) (2020.6.20) >> Requirement already satisfied: idna<3,>=2.5 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests<=2.23.0->scipion-pyworkflow) (2.10) >> Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests<=2.23.0->scipion-pyworkflow) (1.25.11) >> Requirement already satisfied: chardet<4,>=3.0.2 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests<=2.23.0->scipion-pyworkflow) (3.0.4) >> Requirement already satisfied: future>=0.16.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) >> Requirement already satisfied: six in >> ./.scipion3env/lib/python3.5/site-packages (from >> cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) >> Requirement already satisfied: setuptools in >> ./.scipion3env/lib/python3.5/site-packages (from >> kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2) >> DEPRECATION: Python 3.5 reached the end of its life on September 13th, >> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip >> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove >> support for this functionality. >> Requirement already satisfied: scipion-app in >> ./.scipion3env/lib/python3.5/site-packages (3.0.5) >> Requirement already satisfied: outdated==0.2.0 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0) >> Requirement already satisfied: scipion-em in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4) >> Requirement already satisfied: littleutils in >> ./.scipion3env/lib/python3.5/site-packages (from >> outdated==0.2.0->scipion-app) (0.2.2) >> Requirement already satisfied: requests in >> ./.scipion3env/lib/python3.5/site-packages (from >> outdated==0.2.0->scipion-app) (2.23.0) >> Requirement already satisfied: scipion-pyworkflow in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) >> (3.0.5) >> Requirement already satisfied: biopython==1.76 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) >> (1.76) >> Requirement already satisfied: idna<3,>=2.5 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests->outdated==0.2.0->scipion-app) (2.10) >> Requirement already satisfied: chardet<4,>=3.0.2 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests->outdated==0.2.0->scipion-app) (3.0.4) >> Requirement already satisfied: certifi>=2017.4.17 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests->outdated==0.2.0->scipion-app) (2020.6.20) >> Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> requests->outdated==0.2.0->scipion-app) (1.25.11) >> Requirement already satisfied: matplotlib<=3.2.2 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (3.0.3) >> Requirement already satisfied: configparser<=5.0.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (4.0.2) >> Requirement already satisfied: numpy<=1.18.4 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) >> Requirement already satisfied: pillow<=7.1.2 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) >> Requirement already satisfied: bibtexparser<=1.2.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) >> Requirement already satisfied: psutil<=5.7.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) >> Requirement already satisfied: cycler>=0.10 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >> in ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) >> Requirement already satisfied: python-dateutil>=2.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) >> Requirement already satisfied: kiwisolver>=1.0.1 in >> ./.scipion3env/lib/python3.5/site-packages (from >> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0) >> Requirement already satisfied: future>=0.16.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) >> Requirement already satisfied: six in >> ./.scipion3env/lib/python3.5/site-packages (from >> cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) >> (1.15.0) >> Requirement already satisfied: setuptools in >> ./.scipion3env/lib/python3.5/site-packages (from >> kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) >> (50.3.2) >> Scipion v3.0.5 () devel >> >> >>> WARNING: Image library not found! >> > Please install Xmipp to get full functionality. >> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin >> manager window) >> >> >> Building scipion-em-xmipp ... >> /home/hilvertg/tetterst/.scipion3env/bin/python -m pip install >> scipion-em-xmipp==20.7.1 >> DEPRECATION: Python 3.5 reached the end of its life on September 13th, >> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip >> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove >> support for this functionality. >> Requirement already satisfied: scipion-em-xmipp==20.7.1 in >> ./.scipion3env/lib/python3.5/site-packages (20.7.1) >> Requirement already satisfied: joblib in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) >> (0.14.1) >> Requirement already satisfied: peppercorn in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) >> (0.6) >> Requirement already satisfied: plotter in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) >> (1.3.17) >> Requirement already satisfied: scons in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) >> (4.0.1) >> Requirement already satisfied: scikit-learn==0.22.1 in >> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) >> (0.22.1) >> Requirement already satisfied: setuptools in >> ./.scipion3env/lib/python3.5/site-packages (from >> scons->scipion-em-xmipp==20.7.1) (50.3.2) >> Requirement already satisfied: scipy>=0.17.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1) >> Requirement already satisfied: numpy>=1.11.0 in >> ./.scipion3env/lib/python3.5/site-packages (from >> scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4) >> Done (0.36 seconds) >> Building xmippSrc-3.20.07 ... >> Skipping command: wget -nv -c -O >> /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part >> http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz >> mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part >> /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz >> All targets exist. >> Skipping command: tar -xf xmippSrc-v3.20.07.tgz >> All targets exist. >> cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07 >> cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp >> compileAndInstall N=4 && ln -srfn build >> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch >> installation_finished && rm bindings_linked 2> /dev/null >> Traceback (most recent call last): >> File "./xmipp", line 1753, in <module> >> XMIPP_SCRIPT_VERSION = getScriptVersion() >> File "./xmipp", line 1718, in getScriptVersion >> return lastCommit[0].strip() >> IndexError: list index out of range >> Traceback (most recent call last): >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", >> line 453, in <module> >> main() >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", >> line 296, in main >> installPluginMethods() >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", >> line 231, in installPluginMethods >> plugin.installBin({'args': ['-j', numberProcessor]}) >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> environment.execute() >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", >> line 748, in execute >> self._executeTargets(targetList) >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> tgt.execute() >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", >> line 220, in execute >> command.execute() >> File >> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", >> line 161, in execute >> "running '%s')" % (t, cmd)) >> AssertionError: target >> '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' >> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp >> check_config && ./xmipp compileAndInstall N=4 && ln -srfn build >> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch >> installation_finished && rm bindings_linked 2> /dev/null') >> Error at main: target >> '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' >> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp >> check_config && ./xmipp compileAndInstall N=4 && ln -srfn build >> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch >> installation_finished && rm bindings_linked 2> /dev/null') >> >> Something went wrong running: >> cd /home/hilvertg/tetterst && >> /usr/bin/python3 -m virtualenv --python=python3 .scipion3env && >> . /home/hilvertg/tetterst/.scipion3env/bin/activate && >> cd /home/hilvertg/tetterst && >> mkdir -p software/lib && >> mkdir -p software/bindings && >> mkdir -p software/em && >> export SCIPION_HOME=/home/hilvertg/tetterst && >> pip install scipion-pyworkflow && >> pip install scipion-app && >> python -m scipion installp -p scipion-em-xmipp -j 4 >> Installation cancelled. >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Moustafa, I. M. <ri...@ps...> - 2020-10-29 16:48:03
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Many thanks David! downgrading numpy to version 1.18.4 solved the issue. Now Scipion3 can launch the gui. Pablo: I see localrec indicated as installed plugin in the plugins manager. Still puzzled why it did not build in the site-packages under .scipionenv directory! Not sure if that affects localrec or it can still work properly. The output of scipion3 printenv is shown below. If it needs edit please let me know! Scipion v3.0.5 () devel export CUDA_BIN="/opt/debian10/cuda/10.1.243/bin" export CUDA_LIB="/opt/debian10/cuda/10.1.243/lib64" export EMAN2_HOME="/usr/local/scipion/software/em/eman-2.31" export EMFACILITIES_HOME="/usr/local/scipion" export EM_ROOT="software/em" export LOCSCALE_HOME="/usr/local/scipion/software/em/locscale-0.1" export MAXIT_HOME="/usr/local/scipion/software/em/maxit-10.1" export OPENCV="False" export RELION_HOME="/usr/local/scipion/software/em/relion-3.1.0" export SCIPION_CONFIG="/usr/local/scipion/config/scipion.conf" export SCIPION_CWD="/home/ria2" export SCIPION_DOMAIN="pwem" export SCIPION_FONT_NAME="Helvetica" export SCIPION_HOME="/usr/local/scipion" export SCIPION_HOSTS="/usr/local/scipion/config/hosts.conf" export SCIPION_LOCAL_CONFIG="/home/ria2/.config/scipion/scipion.conf" export SCIPION_LOG="/storage/ria2/ScipionUserData/logs/scipion.log" export SCIPION_LOGO="scipion_logo.gif" export SCIPION_LOGS="/storage/ria2/ScipionUserData/logs" export SCIPION_NOTES_ARGS="" export SCIPION_NOTES_FILE="notes.txt" export SCIPION_NOTES_PROGRAM="" export SCIPION_NOTIFY="False" export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/" export SCIPION_PROTOCOLS="/usr/local/scipion/config/protocols.conf" export SCIPION_SOFTWARE="/usr/local/scipion/software" export SCIPION_SUPPORT_EMAIL="sc...@cn..." export SCIPION_TESTS="/usr/local/scipion/data/tests" export SCIPION_TESTS_CMD="scipion3 tests" export SCIPION_TESTS_OUTPUT="/usr/local/scipion/Tests" export SCIPION_TMP="/storage/ria2/ScipionUserData/tmp" export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion" export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software" export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests" export SCIPION_USER_DATA="/storage/ria2/ScipionUserData" export SCIPION_VERSION="v3.0.5 () devel" export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]" export XMIPP2_HOME="/usr/local/scipion/software/em/Xmipp-2.4-src" export XMIPP_HOME="/usr/local/scipion/software/em/xmipp" Thanks, Ibrahim ________________________________ From: David Maluenda <dma...@cn...> Sent: Thursday, October 29, 2020 6:48 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] problem installing scipion3 The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by ./scipion3 python -m pip install numpy==1.18.4 Hope it helps, Regards, <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fucm.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004301017%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=85csE4HN%2BamymeYf96qZGBrQ9Lpe2TdyNiWtvzMyy7U%3D&reserved=0> _____ Dr. David Maluenda Niubó dma...@cn...<mailto:dma...@cn...> - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cnb.csic.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6kFNVSCUIjY9yH8KWZdNRtX2stnOT92uoobn3EWhseo%3D&reserved=0> BioComputing Unit<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiocomputingunit.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4PytI0mGWheRX0qMHZc1runOa3ipTB5axLBZ6bZMwjs%3D&reserved=0> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote: I think now localrec is installed depite the error message and xmipp looks fixed too. Could you please send the output of: scipion3 printenv On 29/10/20 4:18, Moustafa, Ibrahim M. wrote: Hi David, I appreciate your help. I tried what you suggested, removed xmipp and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It compiled with no error. I re-installed scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error: Successfully installed scipion-em-localrec-3.0.1 Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> main() File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main installPluginMethods() File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods installed = plugin.installPipModule(version=pluginVersion) File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule environment.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute command.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1') Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1') No idea why it could not build in the site-packages directory (which I own)! Now if I run: 'scipion3 inspect localrec' I get the following: Scipion v3.0.5 () devel Plugin: localrec >>> constants: loaded >>> convert: loaded >>> protocols: loaded >>> wizards: missing >>> viewers: loaded >>> tests: loaded I also still not able to run Scipion3, I get the following error: Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> main() File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main ProjectManagerWindow().show() File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__ ProjectBaseWindow.__init__(self, title, minsize=(750, 500), File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__ Window.__init__(self, title, masterWindow, weight=weight, File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__ pw.Config.getDomain()._discoverGUIPlugins() File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins entry_point.load() File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load self.require(*args, **kwargs) File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require items = working_set.resolve(reqs, env, installer, extras=self.extras) File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'}) Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'}) Any suggestion to get this fixed is appreciated! Thanks, Ibrahim ________________________________ From: David Maluenda <dma...@cn...><mailto:dma...@cn...> Sent: Wednesday, October 28, 2020 2:32 PM To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...> Subject: Re: [scipion-users] problem installing scipion3 Hi, The error depicted above sounds me. I think it's raised when the xmipp plugin version is not sync with the xmipp software version. Please, try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8' Hope it helps. Regards, _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub...<mailto:dma...@ub...> Wavefront Engineering Group Applied Physics (UB) El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> escribió: Running "scipion3 inspect localrec" gives the following error: Scipion v3.0.5 () devel >>> WARNING: Image library not found! > Please install Xmipp to get full functionality. (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) Plugin: localrec >>> constants: loaded >>> convert: loaded >>> protocols: loaded >>> wizards: missing >>> viewers: loaded >>> tests: error -> Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule m = importlib.import_module('%s.%s' % (name, subname)) File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1014, in _gcd_import File "<frozen importlib._bootstrap>", line 991, in _find_and_load File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 671, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 783, in exec_module File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module> from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase, File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module> from xmipp3.protocols import XmippProtCreateMask3D File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module> from .protocol_ctf_micrographs import XmippProtCTFMicrographs File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module> from xmipp3.base import isMdEmpty ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py) Ibrahim ________________________________ From: Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> Sent: Wednesday, October 28, 2020 2:23 AM To: sci...@li...<mailto:sci...@li...> <sci...@li...<mailto:sci...@li...>> Subject: Re: [scipion-users] problem installing scipion3 Despite the error, it seems localrec is installed. What about: ./scipion3 inspect localrec On 27/10/20 19:12, Moustafa, Ibrahim M. wrote: scipion-em-localrec 3.0.1 -- Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FjnNlurCxbneNXwp7bE3txsqZK8VC2JELVR%2Fvxl2FBc%3D&reserved=0> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004321001%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ygQiTpaQhhAPZskDNurYuAACI%2BM5mZ%2Fn8g%2FDuBss0yI%3D&reserved=0> _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004330999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=cKPih6fvBenoVP0i36Y7FHkkS2zCssv3GhWgehsI8%2BA%3D&reserved=0> -- Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004330999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=0wiCQk7AJ%2BYI12ia1td%2F9JOkXWNyF8IaRaSiSpVWXxI%3D&reserved=0> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004340993%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rQsW3fVv1XKn6tJYefhAzJGiawp2dWzxejIw5ZhhUaw%3D&reserved=0> |
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From: David <dst...@cn...> - 2020-10-29 15:22:16
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Hi, other option is to set these directly in the xmipp.conf file (located in your xmipp install folder, typically 'xmipp-bundle'), and then recompile xmipp (typically 'scipion3 run path_to_xmipp_script_in_xmipp-bundle'). The problem is gonna be our default optimization flags (-mtune=native -march=native). It should be enough to remove them. KR, David S. On 29/10/20 16:11, Carlos Oscar Sorzano wrote: > > Dear Wolfgang, > > in the compilation of Xmipp, you can set the environment variable > CXXFLAGS before calling the xmipp script. From the Scipion > installation I am not sure how to pass it to the xmipp script. It may > be that setting it in the shell before calling scipion suffices. But I > have never tried. > > Kind regards, Carlos Oscar > > El 29/10/2020 a las 11:13, Pablo Conesa escribió: >> >> ? >> >> >> >> -------- Forwarded Message -------- >> Subject: [scipion-users] scipion-installer - how do i change >> compiler optimization flags? >> Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) >> From: Lugmayr, Wolfgang <w.l...@uk...> >> Reply-To: Mailing list for Scipion users >> <sci...@li...> >> To: Mailing list for Scipion users >> <sci...@li...> >> >> >> >> hi, >> >> i installed and compiled scipion 3.0.5-devel on a system with intel cpus. >> >> when i run now scipion on new nodes with "AMD EPYC 7402" processors >> the executable fails with: >> $ scipion3 last Scipion v3.0.5 () devel >> sh: line 1: 45875 Illegal instruction python -m scipion last >> >> so i do not want to have 2 versions of scipion3 but maybe compile it >> with intel and amd compatibility flags. >> how do i set these flags? >> >> cheers, >> wolfgang >> >> -- >> Universitätsklinikum Hamburg-Eppendorf (UKE) >> @ Centre for Structral Systems Biology (CSSB) >> @ Deutsches Elektronen-Synchrotron (DESY) >> Notkestrasse 85 Gebäude 15 >> 22607 Hamburg, Germany >> Tel.: +49 40 8998-87652 >> Email:wol...@cs... >> http://www.cssb-hamburg.de/ >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2020-10-29 15:11:43
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Dear Wolfgang, in the compilation of Xmipp, you can set the environment variable CXXFLAGS before calling the xmipp script. From the Scipion installation I am not sure how to pass it to the xmipp script. It may be that setting it in the shell before calling scipion suffices. But I have never tried. Kind regards, Carlos Oscar El 29/10/2020 a las 11:13, Pablo Conesa escribió: > > ? > > > > -------- Forwarded Message -------- > Subject: [scipion-users] scipion-installer - how do i change compiler > optimization flags? > Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET) > From: Lugmayr, Wolfgang <w.l...@uk...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > To: Mailing list for Scipion users <sci...@li...> > > > > hi, > > i installed and compiled scipion 3.0.5-devel on a system with intel cpus. > > when i run now scipion on new nodes with "AMD EPYC 7402" processors > the executable fails with: > $ scipion3 last Scipion v3.0.5 () devel > sh: line 1: 45875 Illegal instruction python -m scipion last > > so i do not want to have 2 versions of scipion3 but maybe compile it > with intel and amd compatibility flags. > how do i set these flags? > > cheers, > wolfgang > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Deutsches Elektronen-Synchrotron (DESY) > Notkestrasse 85 Gebäude 15 > 22607 Hamburg, Germany > Tel.: +49 40 8998-87652 > Email:wol...@cs... > http://www.cssb-hamburg.de/ > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Tetter S. <tet...@or...> - 2020-10-29 14:20:04
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Dear Grigory,
Step 4 does indeed cause trouble:
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
What does that mean?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...>
Gesendet: Mittwoch, 28. Oktober 2020 10:38:04
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
Hi Tetter,
Could you try the following steps manually:
1) conda activate .scipion3env
2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
3) rm -f xmipp.conf
4) ./xmipp config
5) ./xmipp check_config
6) ./xmipp compileAndInstall N=4
7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp
If you have errors in step 4, please post it here.
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...<mailto:tet...@or...>> wrote:
Dear all,
I am trying to install Scipion for single particle analysis, and more specifically for symmetry relaxation. Unfortunately I can't seem to get the installation to work. I am working with Ubuntu 16.04. Please be aware that I am not a well-versed Ubuntu user.
I have tried installation both via the conda version and the virtualenv version described on https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation, but they both fail eventually. (I have changed the export PATH line to point to sr/local/cuda-9.0/bin to fit my setup.)
Below is what happens. Any ideas?
Thanks,
Stephan
hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev openjdk-8-jdk
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libtiff5-dev' instead of 'libtiff-dev'
g++ is already the newest version (4:5.3.1-1ubuntu1).
gcc is already the newest version (4:5.3.1-1ubuntu1).
libfftw3-dev is already the newest version (3.3.4-2ubuntu1).
libjpeg-dev is already the newest version (8c-2ubuntu8).
make is already the newest version (4.1-6).
python3-tk is already the newest version (3.5.1-1).
libopenmpi-dev is already the newest version (1.10.2-8ubuntu1).
libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5).
libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7).
openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04).
libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1).
0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin
hilvertg@bamf:~$ python -m pip install --user scipion-installerRequirement already satisfied: scipion-installer in ./.local/lib/python2.7/site-packages (1.0.9)
Requirement already satisfied: virtualenv in ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0)
Requirement already satisfied: six<2,>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer) (1.10.0)
Requirement already satisfied: appdirs<2,>=1.4.3 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (1.4.4)
Requirement already satisfied: distlib<1,>=0.3.1 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (0.3.1)
Requirement already satisfied: importlib-resources>=1.0; python_version < "3.7" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.2.0)
Requirement already satisfied: importlib-metadata<3,>=0.12; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.0.0)
Requirement already satisfied: filelock<4,>=3.0.0 in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (3.0.12)
Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer) (2.3.5)
Requirement already satisfied: typing; python_version < "3.5" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3)
Requirement already satisfied: contextlib2; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1)
Requirement already satisfied: zipp>=0.4; python_version < "3.8" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (1.2.0)
Requirement already satisfied: singledispatch; python_version < "3.4" in ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0; python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3)
Requirement already satisfied: configparser>=3.5; python_version < "3" in ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12; python_version < "3.8"->virtualenv->scipion-installer) (4.0.2)
Requirement already satisfied: scandir; python_version < "3.5" in /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3; python_version < "3.4" and sys_platform != "win32"->virtualenv->scipion-installer) (1.9.0)
hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created virtual environment CPython3.5.2.final.0-64 in 99ms
creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env, clear=False, global=False)
seeder FromAppData(download=False, wheel=bundle, setuptools=bundle, pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv)
added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0, biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2, cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1, kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4, outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17, psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0, scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4, scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1, setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1
activators PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0)
Requirement already satisfied: requests<=2.23.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (2.23.0)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.11)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2)
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-app in ./.scipion3env/lib/python3.5/site-packages (3.0.5)
Requirement already satisfied: outdated==0.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0)
Requirement already satisfied: scipion-em in ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4)
Requirement already satisfied: littleutils in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (0.2.2)
Requirement already satisfied: requests in ./.scipion3env/lib/python3.5/site-packages (from outdated==0.2.0->scipion-app) (2.23.0)
Requirement already satisfied: scipion-pyworkflow in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (3.0.5)
Requirement already satisfied: biopython==1.76 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app) (1.76)
Requirement already satisfied: idna<3,>=2.5 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./.scipion3env/lib/python3.5/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20)
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Requirement already satisfied: matplotlib<=3.2.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.0.3)
Requirement already satisfied: configparser<=5.0.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (4.0.2)
Requirement already satisfied: numpy<=1.18.4 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4)
Requirement already satisfied: pillow<=7.1.2 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0)
Requirement already satisfied: psutil<=5.7.0 in ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0)
Requirement already satisfied: cycler>=0.10 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.scipion3env/lib/python3.5/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0)
Requirement already satisfied: future>=0.16.0 in ./.scipion3env/lib/python3.5/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2)
Requirement already satisfied: six in ./.scipion3env/lib/python3.5/site-packages (from cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (50.3.2)
Scipion v3.0.5 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Building scipion-em-xmipp ...
/home/hilvertg/tetterst/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7.1
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
Requirement already satisfied: scipion-em-xmipp==20.7.1 in ./.scipion3env/lib/python3.5/site-packages (20.7.1)
Requirement already satisfied: joblib in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.14.1)
Requirement already satisfied: peppercorn in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.6)
Requirement already satisfied: plotter in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (1.3.17)
Requirement already satisfied: scons in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (4.0.1)
Requirement already satisfied: scikit-learn==0.22.1 in ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1) (0.22.1)
Requirement already satisfied: setuptools in ./.scipion3env/lib/python3.5/site-packages (from scons->scipion-em-xmipp==20.7.1) (50.3.2)
Requirement already satisfied: scipy>=0.17.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1)
Requirement already satisfied: numpy>=1.11.0 in ./.scipion3env/lib/python3.5/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4)
Done (0.36 seconds)
Building xmippSrc-3.20.07 ...
Skipping command: wget -nv -c -O /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz
mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz
All targets exist.
Skipping command: tar -xf xmippSrc-v3.20.07.tgz
All targets exist.
cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null
Traceback (most recent call last):
File "./xmipp", line 1753, in <module>
XMIPP_SCRIPT_VERSION = getScriptVersion()
File "./xmipp", line 1718, in getScriptVersion
return lastCommit[0].strip()
IndexError: list index out of range
Traceback (most recent call last):
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 453, in <module>
main()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py", line 161, in execute
"running '%s')" % (t, cmd))
AssertionError: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srfn build /home/hilvertg/tetterst/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Something went wrong running:
cd /home/hilvertg/tetterst &&
/usr/bin/python3 -m virtualenv --python=python3 .scipion3env &&
. /home/hilvertg/tetterst/.scipion3env/bin/activate &&
cd /home/hilvertg/tetterst &&
mkdir -p software/lib &&
mkdir -p software/bindings &&
mkdir -p software/em &&
export SCIPION_HOME=/home/hilvertg/tetterst &&
pip install scipion-pyworkflow &&
pip install scipion-app &&
python -m scipion installp -p scipion-em-xmipp -j 4
Installation cancelled.
_______________________________________________
scipion-users mailing list
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From: David M. <dma...@cn...> - 2020-10-29 10:49:35
|
The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by ./scipion3 python -m pip install numpy==1.18.4 Hope it helps, Regards, <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <pc...@cn...> wrote: > I think now localrec is installed depite the error message and xmipp > looks fixed too. > > > Could you please send the output of: > > > scipion3 printenv > > > > On 29/10/20 4:18, Moustafa, Ibrahim M. wrote: > > Hi David, > > I appreciate your help. I tried what you suggested, removed xmipp and > used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It > compiled with no error. > I re-installed scipion-em-localrec 'scipion installp -p > scipion-em-localrec' and I still get the following error: > > Successfully installed scipion-em-localrec-3.0.1Traceback (most recent call last): File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> main() File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main installPluginMethods() File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods installed = plugin.installPipModule(version=pluginVersion) File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule environment.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() > File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute command.execute() File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute assert glob(t), ("target '%s' not built (after "AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1') > > > No idea why it could not build in the site-packages directory (which I > own)! > > Now if I run: 'scipion3 inspect localrec' I get the following: > Scipion v3.0.5 () devel > Plugin: localrec > >>> constants: loaded > >>> convert: loaded > >>> protocols: loaded > >>> wizards: missing > >>> viewers: loaded > >>> tests: loaded > > I also still not able to run Scipion3, I get the following error: > Traceback (most recent call last): > File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module> > main() > File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main > ProjectManagerWindow().show() > File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line > 391, in __init__ > ProjectBaseWindow.__init__(self, title, minsize=(750, 500), > File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, > in __init__ > Window.__init__(self, title, masterWindow, weight=weight, > File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in > __init__ > pw.Config.getDomain()._discoverGUIPlugins() > File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in > _discoverGUIPlugins > entry_point.load() > File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in > load > self.require(*args, **kwargs) > File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in > require > items = working_set.resolve(reqs, env, installer, extras=self.extras) > File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in > resolve > raise VersionConflict(dist, req).with_context(dependent_req) > pkg_resources.ContextualVersionConflict: (numpy 1.19.2 > (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), > {'scipion-pyworkflow'}) > Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), > Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'}) > > > Any suggestion to get this fixed is appreciated! > > Thanks, > Ibrahim > > > > ------------------------------ > *From:* David Maluenda <dma...@cn...> <dma...@cn...> > *Sent:* Wednesday, October 28, 2020 2:32 PM > *To:* Mailing list for Scipion users <sci...@li...> > <sci...@li...> > *Subject:* Re: [scipion-users] problem installing scipion3 > > Hi, > > The error depicted above sounds me. I think it's raised when the xmipp > plugin version is not sync with the xmipp software version. Please, try to > remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8' > > > Hope it helps. > > Regards, > > _____ > Dr. David Maluenda Niubó > (+34) 619.029.310 - dma...@ub... > Wavefront Engineering Group > Applied Physics (UB) > > El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...> escribió: > > Running "scipion3 inspect localrec" gives the following error: > > Scipion v3.0.5 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Plugin: localrec > >>> constants: loaded > >>> convert: loaded > >>> protocols: loaded > >>> wizards: missing > >>> viewers: loaded > >>> tests: error -> Traceback (most recent call last): > File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line > 74, in getSubmodule > m = importlib.import_module('%s.%s' % (name, subname)) > File > "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", > line 127, in import_module > return _bootstrap._gcd_import(name[level:], package, level) > File "<frozen importlib._bootstrap>", line 1014, in _gcd_import > File "<frozen importlib._bootstrap>", line 991, in _find_and_load > File "<frozen importlib._bootstrap>", line 975, in > _find_and_load_unlocked > File "<frozen importlib._bootstrap>", line 671, in _load_unlocked > File "<frozen importlib._bootstrap_external>", line 783, in exec_module > File "<frozen importlib._bootstrap>", line 219, in > _call_with_frames_removed > File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in > <module> > from .test_protocol_localized_reconstruction import > (TestLocalizedReconsBase, > File > "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", > line 37, in <module> > from xmipp3.protocols import XmippProtCreateMask3D > File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in > <module> > from .protocol_ctf_micrographs import XmippProtCTFMicrographs > File > "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line > 44, in <module> > from xmipp3.base import isMdEmpty > ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' > (/usr/local/scipion/pip/xmipp3/base.py) > > Ibrahim > ------------------------------ > *From:* Pablo Conesa <pc...@cn...> > *Sent:* Wednesday, October 28, 2020 2:23 AM > *To:* sci...@li... < > sci...@li...> > *Subject:* Re: [scipion-users] problem installing scipion3 > > > Despite the error, it seems localrec is installed. > > What about: > > ./scipion3 inspect localrec > > > On 27/10/20 19:12, Moustafa, Ibrahim M. wrote: > > scipion-em-localrec 3.0.1 > > -- > Pablo Conesa - *Madrid Scipion > <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2B7iKfpsv7zLReOANbRzG1IUSaNvs5lD%2B3%2Fr%2F9K04M5Y%3D&reserved=0> > team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=ubjyOXExNvy2Ac3v4k9WZCPZaQu4%2Fy8xrXb5U5DqKUw%3D&reserved=0> > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2020-10-29 10:16:24
|
I think now localrec is installed depite the error message and xmipp
looks fixed too.
Could you please send the output of:
scipion3 printenv
On 29/10/20 4:18, Moustafa, Ibrahim M. wrote:
> Hi David,
>
> I appreciate your help. I tried what you suggested, removed xmipp
> and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option.
> It compiled with no error.
> I re-installed scipion-em-localrec 'scipion installp -p
> scipion-em-localrec' and I still get the following error:
>
> Successfully installed scipion-em-localrec-3.0.1
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
> installPluginMethods()
> File "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethods
> installed = plugin.installPipModule(version=pluginVersion)
> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line
> 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in
> execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in
> _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in
> execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in
> execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
> scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
> scipion-em-localrec==3.0.1')
>
> No idea why it could not build in the site-packages directory (which I
> own)!
>
> Now if I run: 'scipion3 inspect localrec' I get the following:
> Scipion v3.0.5 () devel
> Plugin: localrec
> >>> constants: loaded
> >>> convert: loaded
> >>> protocols: loaded
> >>> wizards: missing
> >>> viewers: loaded
> >>> tests: loaded
>
> I also still not able to run Scipion3, I get the following error:
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main
> ProjectManagerWindow().show()
> File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py",
> line 391, in __init__
> ProjectBaseWindow.__init__(self, title, minsize=(750, 500),
> File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line
> 53, in __init__
> Window.__init__(self, title, masterWindow, weight=weight,
> File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in
> __init__
> pw.Config.getDomain()._discoverGUIPlugins()
> File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in
> _discoverGUIPlugins
> entry_point.load()
> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446,
> in load
> self.require(*args, **kwargs)
> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469,
> in require
> items = working_set.resolve(reqs, env, installer, extras=self.extras)
> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775,
> in resolve
> raise VersionConflict(dist, req).with_context(dependent_req)
> pkg_resources.ContextualVersionConflict: (numpy 1.19.2
> (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'),
> {'scipion-pyworkflow'})
> Error at main: (numpy 1.19.2 (/usr/local/scipion/pip),
> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>
>
> Any suggestion to get this fixed is appreciated!
>
> Thanks,
> Ibrahim
>
>
>
> ------------------------------------------------------------------------
> *From:* David Maluenda <dma...@cn...>
> *Sent:* Wednesday, October 28, 2020 2:32 PM
> *To:* Mailing list for Scipion users <sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> Hi,
>
> The error depicted above sounds me. I think it's raised when the xmipp
> plugin version is not sync with the xmipp software version. Please,
> try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8'
>
>
> Hope it helps.
>
> Regards,
>
> _____
> Dr. David Maluenda Niubó
> (+34) 619.029.310 - dma...@ub... <mailto:dma...@ub...>
> Wavefront Engineering Group
> Applied Physics (UB)
>
> El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...
> <mailto:ri...@ps...>> escribió:
>
> Running "scipion3 inspect localrec" gives the following error:
>
> Scipion v3.0.5 () devel
>
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion
> plugin manager window)
>
>
> Plugin: localrec
> >>> constants: loaded
> >>> convert: loaded
> >>> protocols: loaded
> >>> wizards: missing
> >>> viewers: loaded
> >>> tests: error -> Traceback (most recent call last):
> File
> "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line
> 74, in getSubmodule
> m = importlib.import_module('%s.%s' % (name, subname))
> File
> "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py",
> line 127, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
> File "<frozen importlib._bootstrap>", line 991, in _find_and_load
> File "<frozen importlib._bootstrap>", line 975, in
> _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 783, in
> exec_module
> File "<frozen importlib._bootstrap>", line 219, in
> _call_with_frames_removed
> File "/usr/local/scipion/pip/localrec/tests/__init__.py", line
> 27, in <module>
> from .test_protocol_localized_reconstruction import
> (TestLocalizedReconsBase,
> File
> "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py",
> line 37, in <module>
> from xmipp3.protocols import XmippProtCreateMask3D
> File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line
> 50, in <module>
> from .protocol_ctf_micrographs import XmippProtCTFMicrographs
> File
> "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py",
> line 44, in <module>
> from xmipp3.base import isMdEmpty
> ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base'
> (/usr/local/scipion/pip/xmipp3/base.py)
>
> Ibrahim
> ------------------------------------------------------------------------
> *From:* Pablo Conesa <pc...@cn...
> <mailto:pc...@cn...>>
> *Sent:* Wednesday, October 28, 2020 2:23 AM
> *To:* sci...@li...
> <mailto:sci...@li...>
> <sci...@li...
> <mailto:sci...@li...>>
> *Subject:* Re: [scipion-users] problem installing scipion3
>
> Despite the error, it seems localrec is installed.
>
> What about:
>
> ./scipion3 inspect localrec
>
>
> On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:
>> scipion-em-localrec 3.0.1
> --
> Pablo Conesa - *Madrid Scipion
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2B7iKfpsv7zLReOANbRzG1IUSaNvs5lD%2B3%2Fr%2F9K04M5Y%3D&reserved=0>
> team*
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=ubjyOXExNvy2Ac3v4k9WZCPZaQu4%2Fy8xrXb5U5DqKUw%3D&reserved=0>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Moustafa, I. M. <ri...@ps...> - 2020-10-29 03:19:10
|
Hi David,
I appreciate your help. I tried what you suggested, removed xmipp and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It compiled with no error.
I re-installed scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error:
Successfully installed scipion-em-localrec-3.0.1
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
installPluginMethods()
File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods
installed = plugin.installPipModule(version=pluginVersion)
File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule
environment.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute
command.execute()
File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1')
No idea why it could not build in the site-packages directory (which I own)!
Now if I run: 'scipion3 inspect localrec' I get the following:
Scipion v3.0.5 () devel
Plugin: localrec
>>> constants: loaded
>>> convert: loaded
>>> protocols: loaded
>>> wizards: missing
>>> viewers: loaded
>>> tests: loaded
I also still not able to run Scipion3, I get the following error:
Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module>
main()
File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main
ProjectManagerWindow().show()
File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__
ProjectBaseWindow.__init__(self, title, minsize=(750, 500),
File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__
Window.__init__(self, title, masterWindow, weight=weight,
File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__
pw.Config.getDomain()._discoverGUIPlugins()
File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins
entry_point.load()
File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load
self.require(*args, **kwargs)
File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
Any suggestion to get this fixed is appreciated!
Thanks,
Ibrahim
________________________________
From: David Maluenda <dma...@cn...>
Sent: Wednesday, October 28, 2020 2:32 PM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
Hi,
The error depicted above sounds me. I think it's raised when the xmipp plugin version is not sync with the xmipp software version. Please, try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8'
Hope it helps.
Regards,
_____
Dr. David Maluenda Niubó
(+34) 619.029.310 - dma...@ub...<mailto:dma...@ub...>
Wavefront Engineering Group
Applied Physics (UB)
El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> escribió:
Running "scipion3 inspect localrec" gives the following error:
Scipion v3.0.5 () devel
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
Plugin: localrec
>>> constants: loaded
>>> convert: loaded
>>> protocols: loaded
>>> wizards: missing
>>> viewers: loaded
>>> tests: error -> Traceback (most recent call last):
File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule
m = importlib.import_module('%s.%s' % (name, subname))
File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module>
from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase,
File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module>
from xmipp3.protocols import XmippProtCreateMask3D
File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module>
from .protocol_ctf_micrographs import XmippProtCTFMicrographs
File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
from xmipp3.base import isMdEmpty
ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py)
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...<mailto:pc...@cn...>>
Sent: Wednesday, October 28, 2020 2:23 AM
To: sci...@li...<mailto:sci...@li...> <sci...@li...<mailto:sci...@li...>>
Subject: Re: [scipion-users] problem installing scipion3
Despite the error, it seems localrec is installed.
What about:
./scipion3 inspect localrec
On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:
scipion-em-localrec 3.0.1
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2B7iKfpsv7zLReOANbRzG1IUSaNvs5lD%2B3%2Fr%2F9K04M5Y%3D&reserved=0> team
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From: David M. <dma...@cn...> - 2020-10-28 18:32:39
|
Hi,
The error depicted above sounds me. I think it's raised when the xmipp
plugin version is not sync with the xmipp software version. Please, try to
remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8'
Hope it helps.
Regards,
_____
Dr. David Maluenda Niubó
(+34) 619.029.310 - dma...@ub...
Wavefront Engineering Group
Applied Physics (UB)
El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...> escribió:
> Running "scipion3 inspect localrec" gives the following error:
>
> Scipion v3.0.5 () devel
>
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin
> manager window)
>
>
> Plugin: localrec
> >>> constants: loaded
> >>> convert: loaded
> >>> protocols: loaded
> >>> wizards: missing
> >>> viewers: loaded
> >>> tests: error -> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line
> 74, in getSubmodule
> m = importlib.import_module('%s.%s' % (name, subname))
> File
> "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py",
> line 127, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
> File "<frozen importlib._bootstrap>", line 991, in _find_and_load
> File "<frozen importlib._bootstrap>", line 975, in
> _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 783, in exec_module
> File "<frozen importlib._bootstrap>", line 219, in
> _call_with_frames_removed
> File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in
> <module>
> from .test_protocol_localized_reconstruction import
> (TestLocalizedReconsBase,
> File
> "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py",
> line 37, in <module>
> from xmipp3.protocols import XmippProtCreateMask3D
> File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in
> <module>
> from .protocol_ctf_micrographs import XmippProtCTFMicrographs
> File
> "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line
> 44, in <module>
> from xmipp3.base import isMdEmpty
> ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base'
> (/usr/local/scipion/pip/xmipp3/base.py)
>
> Ibrahim
> ------------------------------
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Wednesday, October 28, 2020 2:23 AM
> *To:* sci...@li... <
> sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
>
>
> Despite the error, it seems localrec is installed.
>
> What about:
>
> ./scipion3 inspect localrec
>
>
> On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:
>
> scipion-em-localrec 3.0.1
>
> --
> Pablo Conesa - *Madrid Scipion
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Cbf532e8ce14541a85e1908d87b0a12e4%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637394630482954098%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=W46ErzeEGkYXk8Ma7SO5lbA6cfarjSIk9uFY08lcJy8%3D&reserved=0>
> team*
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
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